Geotrichum candidum ATCC 204307 was previously found to generate phenyllactic acid (PLA) and indoleacetic acid (ILA) in complex culture media. In this study, a relationship between concentrations of PLA, ILA, and hydroxy PLA (OH-PLA) and initial concentrations of phenylalanine, tryptophan, and tyrosine, added respectively as unique sources of nitrogen in synthetic medium, was established. Phenylpyruvic acid (PPA), an intermediate compound of PLA metabolism, was able to induce not only PLA but also phenylethyl alcohol (PEA) production when used separately as initial substrate. Under pH, temperature, and salt concentrations used for cheese-making, phenylalanine was found to be the most efficient substrate for antimicrobial metabolite production. In excess of substrate, different yeast strains of Geotrichum candidum, Yarrowia lipolytica, Candida natalensis, and Candida catenulata were shown here to produce 1.6 ± 0.5–5.0 ± 0.2 mM of PLA from phenylalanine, 5.0 ± 0.1–10.9 ± 0.3 mM of ILA from tryptophan, and 1.3 ± 0.3–7.0 ± 0.02 of PLA and 0.1 ± 0.0–2.22 ± 0.09 mM of PEA from PPA. Geotrichum candidum ATCC 204307 was the highest producer. This is the first time these antimicrobial metabolites PLA, OH-PLA, ILA, and PEA are being reported as the reaction products of aromatic amino acids catabolism in G. candidum.